Prevalence of parasites in Alabama poultry flocks with special emphasis on Eimeria maxima

Abstract

Coccidiosis is a disease caused by Eimeria spp. and it is the most prevalent and economically important disease in poultry. Due to its economic importance, the control of coccidiosis is critical. Other parasites can cause disease in chickens but are not as relevant as coccidiosis. Some of these parasites are known zoonoses and can cause disease in humans. It is thought that keeping chickens as backyard pets has become increasingly popular in the United States. Biosecurity is generally low in backyard flocks. As a consequence, they can serve as reservoirs for various pathogens that pose a risk for commercial poultry or human health. For the first part of the thesis, eighty-four fecal samples from 64 backyard chicken flocks throughout the state of Alabama were collected in the summer of 2017 and 2018. Coccidia oocysts were seen in 64.1% of flocks with oocyst counts in most samples below 10,000 oocysts per gram. Eggs of Ascaridia spp. or Heterakis gallinarum were seen in 20.3% of the flocks, and eggs of Capillaria spp. in 26.6% of the flocks. Egg counts were low, rarely exceeding 1,000 eggs per gram. DNA extracted directly from fecal samples was investigated by PCR for other relevant parasites. The results showed that 4.7% of flocks were positive for Histomonas meleagridis, 18.8% of flocks for Tetratrichomonas gallinarum, 18.8% of flocks for Cryptosporidium spp. and 87.5% of flocks for Blastocystis spp..These results will help to provide information that can be used to design outreach programs to improve health and wellbeing of birds in backyard flocks. The aim of the second part of the thesis was to develop a MLST scheme for E. maxima and to compare strains from different farms. Eimeria maxima is a parasite of chickens that can cause coccidiosis and predispose its host to secondary infections. Typing E. maxima is important as some strains have been shown to provide cross protection to one another and have been linked to low performance in broilers. E. maxima isolates have been typed by sequencing the internal transcribed spacer (ITS) region or sequencing the partial cytochrome oxidase I (COI) gene. Multi-locus sequence typing (MLST) is a nucleotide sequence typing system that reflects the population and evolutionary biology of bacterial pathogens, but MLST schemes have also been developed for some eukaryotes. Fecal and litter samples were collected from commercial broiler flocks in Alabama and Tennessee and three fecal samples from backyard flocks were included in the study. Oocysts were isolated from the feces and tested by PCR for E. maxima. Nineteen samples were found positive for E. maxima. Six gene loci that had been identified based on MLST schemes of several different parasites were amplified for these samples and sequenced. Sequences were compared to the reference genome in GenBank. There was more than one allele in all six genes. In three of the genes, insertions and deletions were detected. Mutations were present in coding as well as in non-coding sequences in all genes except one. MLST was able to distinguish two commercially available vaccines and showed that most of the field isolates were not identical to these two vaccines. Backyard strains had different allele variants from vaccine and commercial strains of E. maxima. The results show that MLST is a potential tool for epidemiologic investigation of E. maxima. The information gained from epidemiological investigations using the method will be useful in the development and evaluation of vaccine programs.